I have no clue how this could've happened, but I'm in a real mess right now as I've lost several projects I was currently working on.
I installed a new SSD as my system drive (C), turning my original drive into a scratch disc (E). I have a third, separate drive which has always been my media/projects drive (F). I opened AE and used it for a couple things, then realized I needed to change my media cache or else my SSD would fill up very quickly.
Previously, my media cache was located in the default folder: temp files on the C: drive. ALL of my project files were on my F drive, and autosaving to an external HDD. I told AE to move the cache from C: to my newly formatted E: drive, and went to open up the project file I'd just been working on, only to get an error saying the project wasn't found. I go to look in my projects folder, and every single one of my projects was gone, including the auto-saves on my external. Weirdest of all, the folders themselves are still there, just empty.
The ONLY thing that was done in between working on the project file and it disappearing was changed the cache location. Furthermore, data recovery programs can only find 5 of those files, leaving me up a very smelly creek with no paddle. How could this have happened?
The first and most obvious question is "Where is your back up?"
If you still see any other files that were on the drive that originally contained your project files then I have no idea what happened. If everything on that drive is gone then I suspect you did something weird when you formatted a new drive.
I would never add a new drive to any system without first making sure everything important was backed up. I would highly recommend an external mirrored raid system using Hot swappable drives. By three drives for back up and every few days pop out one of them and slip in the third. In just a few minutes you will have three copies of all your work up to that point. Put the removed drive in a safe place, then repeat the process when you have added a few more projects.